I can think of an excellent reason for Pelini to take the YSU job, and it has NOTHING to do with whether or not YSU is one of top FCS jobs.
To spite Nebraska and stick the screws to them. From all I have read, it seems YSU could pay Pelini $1 per year to be HC until the buyout at Nebraska runs out. Even if he is paid say $150,000 - $200,000, Nebraska would still be paying the vast majority of the money Pelini gets for the next 4+ years.
Taking this job is not without risk for Pelini. If he is not able to beat NDSU consistently, not able to win any of the "money games", and YSU misses the playoffs in ANY season, or is 1 and done or 1-1 at best in playoffs, the knock on him of being unable to guide his team to wins in big games will just get bigger. And, in that case, his HC career will be finished, unless he stays at YSU for 5,10, 15 years and can accept being paid at most $200,000-$250,000, and coaching in front of crowds of 20,000 or less(most of the time more like 10,000, when adding in road games), instead of coaching in stadiums that hold 50,000+, are usually full or 85-90% full, and having most games televised on National TV. not ESPN 3.